Dataset Information

Assessing Habitat Use by Snapper (Chrysophrys auratus) from Baited Underwater Video Data in a Coastal Marine Park.

ABSTRACT: Baited Underwater Video (BUV) systems have become increasingly popular for assessing marine biodiversity. These systems provide video footage from which biologists can identify the individual fish species present. Here we explore the relevance of spatial dependence and marine park boundaries while estimating the distribution and habitat associations of the commercially and recreationally important snapper species Chrysophrys auratus in Moreton Bay Marine Park during a period when new Marine National Parks zoned as no-take or "green" areas (i.e., areas with no legal fishing) were introduced. BUV studies typically enforce a minimum distance among BUV sites, and then assume that observations from different sites are independent conditional on the measured covariates. In this study, we additionally incorporated the spatial dependence among BUV sites into the modelling framework. This modelling approach allowed us to test whether or not the incorporation of highly correlated environmental covariates or the geographic placement of BUV sites produced spatial dependence, which if unaccounted for could lead to model bias. We fitted Bayesian logistic models with and without spatial random effects to determine if the Marine National Park boundaries and available environmental covariates had an effect on snapper presence and habitat preference. Adding the spatial dependence component had little effect on the resulting model parameter estimates that emphasized positive association for particular coastal habitat types by snapper. Strong positive relationships between the presence of snapper and rock habitat, particularly rocky substrate composed of indurated freshwater sediments known as coffee rock, and kelp habitat reinforce the consideration of habitat availability in marine reserve design and the design of any associated monitoring programs.

SUBMITTER: Terres MA

PROVIDER: S-EPMC4552837 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Assessing Habitat Use by Snapper (Chrysophrys auratus) from Baited Underwater Video Data in a Coastal Marine Park.

Terres Maria A MA Lawrence Emma E Hosack Geoffrey R GR Haywood Michael D E MD Babcock Russell C RC

PloS one 20150828 8

Baited Underwater Video (BUV) systems have become increasingly popular for assessing marine biodiversity. These systems provide video footage from which biologists can identify the individual fish species present. Here we explore the relevance of spatial dependence and marine park boundaries while estimating the distribution and habitat associations of the commercially and recreationally important snapper species Chrysophrys auratus in Moreton Bay Marine Park during a period when new Marine Nati ...[more]

PMID: 26317655

Similar Datasets

Project description:Domestication of teleost fish is a recent development, and in most cases started less than 50 years ago. Shedding light on the genomic changes in key economic traits during the domestication process can provide crucial insights into the evolutionary processes involved and help inform selective breeding programmes. Here we report on the recent domestication of a native marine teleost species in New Zealand, the Australasian snapper (Chrysophrys auratus). Specifically, we use genome-wide data from a three-generation pedigree of this species to uncover genetic signatures of domestication selection for growth. Genotyping-By-Sequencing (GBS) was used to generate genome-wide SNP data from a three-generation pedigree to calculate generation-wide averages of FST between every generation pair. The level of differentiation between generations was further investigated using ADMIXTURE analysis and Principal Component Analysis (PCA). After that, genome scans using Bayescan, LFMM and XP-EHH were applied to identify SNP variants under putative selection following selection for growth. Finally, genes near candidate SNP variants were annotated to gain functional insights. Analysis showed that between generations FST values slightly increased as generational time increased. The extent of these changes was small, and both ADMIXTURE analysis and PCA were unable to form clear clusters. Genome scans revealed a number of SNP outliers, indicative of selection, of which a small number overlapped across analyses methods and populations. Genes of interest within proximity of putative selective SNPs were related to biological functions, and revealed an association with growth, immunity, neural development and behaviour, and tumour repression. Even though few genes overlapped between outlier SNP methods, gene functionalities showed greater overlap between methods. While the genetic changes observed were small in most cases, a number of outlier SNPs could be identified, of which some were found by more than one method. Multiple outlier SNPs appeared to be predominately linked to gene functionalities that modulate growth and survival. Ultimately, the results help to shed light on the genomic changes occurring during the early stages of domestication selection in teleost fish species such as snapper, and will provide useful candidates for the ongoing selective breeding in the future of this and related species.

Project description:In Australia and New Zealand (NZ), snapper Chrysophrys auratus is known for delicate mild flavoured flesh and is a favoured species to serve raw as sashimi or in sushi. The diet of snapper includes a variety of intermediate hosts of larval nematodes, and as a result, snapper has potential to become highly infected with zoonotic/non-zoonotic nematodes. The aims of this study were to survey nematodes in snapper from Australia and New Zealand waters and to identify nematode species using combined morphological and molecular methods. The zoonotic potential of nematodes identified in this study are discussed. A total of 112 snapper were purchased from the Sydney fish market, New South Wales, Australia. Fish were dissected and only the visceral content and digestive tract were examined for nematode infection. Parasites were initially identified by the microscopic method as four different types belonging to the families Anisakidae (Anisakis types I & III, and Terranova type II) and Cucullanidae (Dichelyne spp.). All Anisakidae nematodes were at infective stages. Species-level identification was actualised through sequencing of the internal transcribed spacer (ITS-1, 5.8S, ITS-2) regions. The Anisakis types I & III were confirmed as Anisakis pegreffii and A. brevispiculata, respectively of which A. pegreffii is considered globally as a zoonotic nematode. The specific identification of Terranova type II and Dichelyne spp. was not possible as no comparable sequence data were available in GenBank. The phylogenetic tree clustered Anisakis types I & III with A. pegreffii and A. brevispiculata, respectively; Terranova type II sequences as a separate clade with previously identified larval and adult Terranova and Pseudoterranova species. Based on phylogenetic analyses the present Cucullanid specimens were assigned herein as Dichelyne cf. pleuronectidis, and an unknown species Dichelyne sp. 1. This study represents the first host record globally for zoonotic Anisakid nematodes in this popularly consumed table fish and a new region record for D. cf. pleuronectidis and Dichelyne sp. 1. Further investigation is required, using more comprehensive parasite detection and recovery methods, to assess the health risk these nematodes may pose to human and fish health in Australia/NZ.

Project description:Effective sampling of marine communities is essential to provide robust estimates of species richness and abundance. Baited Remote Underwater Video Stations (BRUVS) are a useful tool in assessment of fish assemblages, but research on the optimal sampling period required to record common and rare elasmobranch species is limited. An appropriate 'soak time' (time elapsed between settlement of the BRUVS on the seabed and when it is hauled off the seabed) requires consideration, since longer soak times may be required to record species rare in occurrence, or sightings in areas of generally low elasmobranch abundance. We analysed 5352 BRUVS deployments with a range of soak times across 21 countries in the Coral Triangle and Pacific Ocean, to determine the optimal soak time required for sampling reef-associated elasmobranchs, considering species rarity, and community abundance at each site. Species were categorised into 4 'rarity' groups (very rare to common), by their relative occurrence in the dataset, defined simply by the proportion of BRUVS on which they occurred. Individual BRUVS were categorised into 3 'abundance' groups (low to high) by overall relative elasmobranch abundance, defined as total number of all elasmobranchs sighted per unit of sampling effort. The effects of BRUVS soak times, and levels of rarity and abundance groupings, on the time to first sighting (TFS) and time to maximum number of elasmobranchs observed (tMaxN) were examined. We found that TFS occurred earlier for species groups with high occurrence, and on BRUVS with high elasmobranch abundance, yet longer soak times were not essential to observe rarer species. Our models indicated an optimum of 95% of both sighting event types (TFS, tMaxN) was recorded within 63-77 minutes, and a soak time of 60 minutes recorded 78-94% of the elasmobranch sighting events recorded (78-94% of TFS events and 82-90% of tMaxN events), when species rarity and abundance on BRUVS was accounted for. Our study shows that deployments of ~ 77 minutes are optimal for recording all species we observed, although 60 minutes soak time effectively samples the majority of elasmobranch species in shallow coral reef habitats using BRUVS.

Dataset Information

Assessing Habitat Use by Snapper (Chrysophrys auratus) from Baited Underwater Video Data in a Coastal Marine Park.

Publications

Assessing Habitat Use by Snapper (Chrysophrys auratus) from Baited Underwater Video Data in a Coastal Marine Park.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets